Is CDH11 p.Asp321Tyr (c.961G>T) pathogenic?

CDH11 p.Asp321Tyr (c.961G>T) is classified Uncertain significance in CDH11 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-05-29). AlphaMissense: ambiguous (0.563); Ultra-rare (popmax 0.0835%, amr); Associated with Inborn genetic diseases.

What condition is associated with CDH11 p.Asp321Tyr (c.961G>T)?

CDH11 p.Asp321Tyr (c.961G>T) is associated with Inborn genetic diseases (ClinVar).

How common is CDH11 p.Asp321Tyr (c.961G>T) in the general population?

CDH11 p.Asp321Tyr (c.961G>T) is ultra-rare (popmax 0.0835%, amr) (gnomAD).

What do computational predictors say about CDH11 p.Asp321Tyr (c.961G>T)?

AlphaMissense predicts ambiguous (score 0.563) — an in-silico prediction, not a clinical call.

CDH11 p.Asp321Tyr

c.961G>T · rs749514930 · VCV2356828

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.563 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0835%, amr)

Missense predictors

2/2 damaging

REVEL, SaProt · AlphaMissense no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.563	ambiguous
REVEL	0.658	pathogenic-leaning
SaProt	LLR -12.09	damaging
⇒ REVEL and SaProt both call this damaging; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 2.5, phastCons 1
Regional constraint	o/e 0.90	unconstrained · MANE · 44 kb · p 0.01 · regional, not allelic
Overall
CADD	31.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0835% Admixed American · 50/59,856 alleles

Filtering AF 0.065% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0585%

Overall 0.00316% 51/1,612,608 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0835%	1,197
African / African-American	0.00134%	74,826

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CDH11
Protein: p.Asp321Tyr
Coding: c.961G>T
MANE Select: NM_001797
dbSNP: rs749514930
Type: single nucleotide variant
Location: chr16:64988195 (GRCh38)
Gene constraint: LOEUF 0.249 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 77.65
Residue 321: a UniProt-annotated variant site (in esws); the cadherin 3 domain

Full CDH11 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CDH11 p.Ala228Ser Uncertain significance ★★ ⚠ same condition
CDH11 p.Arg556Trp Uncertain significance ★★ ⚠ same condition
CDH11 p.Gly45Arg Uncertain significance ★★ ⚠ same condition
CDH11 p.Gly618Ser Uncertain significance ★★ ⚠ same condition
CDH11 p.Ile649Val Uncertain significance ★★ ⚠ same condition
CDH11 p.Val478Ile Likely benign ★★ same condition
CDH11 p.Ala470Val Uncertain significance ★ ⚠ same condition
CDH11 p.Ala475Thr Uncertain significance ★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cdh11-p-asp321tyr (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown